Freesurfer

freesurfer@nmr.mgh.harvard.edu

21 participants
30070 discussions

folding index on surface
by Sasha Wolosin 19 Feb '07

19 Feb '07

Dear all, Is it possible to display folding index on the cortical surface? Thanks, Sasha Disclaimer: The materials in this e-mail are private and may contain Protected Health Information. Please note that e-mail is not necessarily confidential or secure. Your use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail.

2 2

coregistration of MRI and MEG
by Sameer Walawalkar 19 Feb '07

19 Feb '07

Hello, I am interested in coregistering mri images with MEG (elekta neuromag 306) data in order to do Dynamic Imaging of Coherent Sources (DICS analysis) using fieldtrip. I have installed freesurfer and have been able to open the mri files. How do I proceed next? Under what title will I be able to find the necessary info on Wiki? Thank you very much in advance for your help. best, sameer

2 1

MNI 305 coordinates to average mesh vertex lookup
by Morgan G. Hough 19 Feb '07

19 Feb '07

Hi there, I was wondering what the best way would be to look up the vertex numbers that correspond to a set of MNI 152 locations we have from a parallel VBM analysis. Lets assume that I have transformed them to MNI 305 coordinates. Can I now do a lookup to get the vertex numbers on my freesurfer average mesh that would best correspond to that MNI 305 location? I see the MNI coordinate of a vertex when I am looking at results in tksurfer but not a way to get the vertex for a particular MNI coordinate. Thanks in advance. Cheers, -Morgan

1 0

RE: [Freesurfer] Reconstruction problems
by Bruce Fischl 17 Feb '07

17 Feb '07

did you look at the surface? You'll probably need to either fix the watershed, or manually disconnect the cerebellum On Wed, 14 Feb 2007, Alex Fornito wrote: > Is there anything that can be done? (e.g., tweaking certain parameters) > > Alex Fornito > JN Peters Research Fellow > Melbourne Neuropsychiatry Centre > National Neuroscience Facility > The University of Melbourne > Levels 2 & 3, 161 Barry St > Carlton South 3053 Vic Australia > Ph: +61 3 8344 1861 > Fax: +61 3 9348 0469 > Email: fornitoa(a)unimelb.edu.au > > > > -----Original Message----- > From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] > Sent: Wednesday, 14 February 2007 2:01 PM > To: Fornito, Alexander > Cc: freesurfer(a)nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] Reconstruction problems > > p.s. also the last defect it gets to is a really big one: > > retessellating defect 105 with 13082 vertices (convex hull=6596). > > which may cause it to run out of memory. In any case, my guess is something > is pretty seriousll wrong with this surface. > > > > On Wed, 14 Feb 2007, Fornito, > Alexander wrote: > >> Hi, >> I'm having problems reconstructing the surface for one individual on an > older version of recon-all (v. 1.104). It always seems to exit with no error > message during mris_fix_topology. I've tried to re-run this subject several > times, and even starting from scratch does not seem to help. I'm not sure > why this is happening, as I've used this version of recon-all on hundreds of > other images without any problem. There's no obvious difference between this > image and any of the others that I can see by looking at the T1 (e.g., no > apparent artifacts, etc.). I've attached recon-all.log. Any suggestions? >> Thanks, >> Alex >> >> Alex Fornito >> JN Peters Research Fellow >> Melbourne Neuropsychiatry Centre and Department of Psychology >> National Neuroscience Facility >> The University of Melbourne Levels 2 & 3, Alan Gilbert Building >> 161 Barry St Carlton South Vic 3053 Australia >> Ph: +61 3 8344 1861 >> Fax: +61 3 9348 0469 >> email: alexander.fornito(a)wh.org.au >> >> >> > > > WARNING: This message originated from outside the Northern/Melbourne/Western > Health e-mail network. The sender cannot be validated. Caution is advised. > Contact IT Services (+61 3) 9342 8888 for more information. > > >

5 9

Re: [Freesurfer] Installation on sun grid]
by Inge K. Amlien 16 Feb '07

16 Feb '07

Bruce: Thank you. Uri: I believe all applications are installed on the compute-nodes via some rollout script at this datacenter. I try not to get into arguments with the IT people on how to configure the computers, but I am sure it is possible to do a central install. It sure would save some space. Have a nice day /Inge On Thu, February 15, 2007 20:04, Uri Hasson wrote: > Hello Inge, > I am curious to know if you are installing FreeSurfer on each > computing node seperately, or in one central location, that is > accessible to all the nodes. We managed to do a central install that > works pretty well at the University of Chicago. > > Best, > Uri > > > On 2/15/07, Inge K. Amlien <ingeam(a)student.sv.uio.no> wrote: >> Hello list, >> we are installing Freesurfer on a computer cluster (about 400 cpu's) >> running the >> Sun Grid Engine. As there are other applications installed on the >> compute >> nodes and space is limited, we would like to strip out any files from >> the >> Freesurfer installation not needed for processing. >> >> Is it safe to remove any files/folders other than the example subjects? >> Tkmedit/tksurfer? >> >> Kind regards >> Inge Kasbohm Amlien >> Department of Psychology >> University of Oslo >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >

1 0

error in brainmask...
by Shahabuddin Ansari 15 Feb '07

15 Feb '07

Hi, Some the processed images have error in their brainmasks (e.g., partial stripping of skull, partial removing of neck and other parts etc.). Is there any way to correct them automatically? Appreciate it. Shahab --------------------------------- Need a quick answer? Get one in minutes from people who know. Ask your question on Yahoo! Answers.

2 1

output orientation incorrect
by Leila BH 15 Feb '07

15 Feb '07

Hello, I am new freesurfer user, I need to have the labels of parcellation on analyze format. I did recon all command on my subject, I see the very beautiful parcellation on freesurfer. After reading all the question/response on the freesurfer website, I write my own txt file describing the 35 labels: I just copy paste the data obtained from the variable colortable.struct_name and colortable.table: the output of read_annotation('rh.aparc.annot'). It seems working correctly, because the mri_annotation2label creates 35 files of all the labels. To check some of them I used tkmedit chuv44 brain.mgz and I loaded one label, it seems good. Is this correct? But when I tried to export this labels to analyze format (readable with mricro for example), I use mri_label2vol: Mri_label2vol -label ./subects/chuv44/mylab/rh.superiorfrontal.label -temp $SUBJECTS_DIR/chuv44/mri/orig/chuv44.img -o ./subjects/chuv44_rh_one.img I had a warning saying that the mat file is missing, and the result orientation is not good. I then open my analyze file with v=spm_vol('chuv44.img') and copy the v.mat as the mat file freesurfer asked for: v.mat ans = -2 0 0 129 0 2 0 -129 0 0 2 -69 0 0 0 1 The command line Mri_label2vol -label ./subects/chuv44/mylab/rh.superiorfrontal.label -temp $SUBJECTS_DIR/chuv44/mri/orig/chuv44.img -o ./subjects/chuv44_rh_one.img works then correctly and write in the end: Analyze output matrix -2 0 0 129 0 2 0 -129 0 0 2 -69 0 0 0 1 --------------------- INFO: set hdr.hist.orient to -1 But when I open the output file chuv44_rh_one.img (analyze) the format is not the same as my image: the axial slice is coronal and vice versa. First question: Is the staff I did with my home-made txt labels_file is correct? And do you know what I should do to obtain my label mask in correct orientation? Thanks in advance Leila Cammoun

1 0

Installation on sun grid
by Inge K. Amlien 15 Feb '07

15 Feb '07

Hello list, we are installing Freesurfer on a computer cluster (about 400 cpu's) running the Sun Grid Engine. As there are other applications installed on the compute nodes and space is limited, we would like to strip out any files from the Freesurfer installation not needed for processing. Is it safe to remove any files/folders other than the example subjects? Tkmedit/tksurfer? Kind regards Inge Kasbohm Amlien Department of Psychology University of Oslo

2 1

how to read 'lh.inflated.asc' using matlab
by r.huang＠fz-juelich.de 15 Feb '07

15 Feb '07

Hello Everyone, I want to know how to load one asc file into matlab. Using mris_convert, I obtained 'rh.lh.sphere.reg.asc'. The procedure is here mris_convert rh.lh.sphere.reg rh.lh.sphere.reg.asc In matlab, when I applied fname='rh.lh.sphere.reg.asc' [S, v, f] = read_asc(fname) the following message comes out [??? Error using ==> reshape To RESHAPE the number of elements must not change. Error in ==> read_asc at 23 f = reshape(f, [5 S(3)])';] Do you know how to solve the problem? Thanks in advance rhuang

1 0

Re: Files uploaded for you on Martinos Center FileDrop site
by Anil Roy 14 Feb '07

14 Feb '07

Here are the details of the acquisitions: Images acquired on a 3T Signa scanner with a standard GE head coil. 3D T1-weighted spiral volume scan (120 slices, 1.4875-mm thick, TR = 20 msec, TE = 6 msec, 40 degrees flip angle, 256 * 192 matrix) The machine has 4 gigs of RAM. Also, AFNI is able to talairach and skull strip. Is there a way I can input the files from AFNI to Freesurfer to resume the recon-all pipeline. Nick, is there a way for me to see your reg so that I can be sure that its not my created xfm that is causing this problem. Thanks, Anil. On 2/14/07, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> wrote: > > why is the background so high? Also, what field strength was this at? > There > looks to be dielectric-like center brightening. The contrast isn't > terrible > though. > > On Wed, 14 Feb 2007, Nick > Schmansky wrote: > > > Bruce, > > > > the orig.mgz can be downloaded via the filedrop, see link in email > > below. > > > > or i have copied it to: > > > > /autofs/space/minerva_001/users/nicks/subjects/anil/mri > > > > N. > > > > > > On Wed, 2007-02-14 at 17:02 -0500, Bruce Fischl wrote: > >> put the .mgz somewhere and I'll take a look. And make sure it's the > >> orig.mgz, which is un-normalized > >> > >> > >> On Wed, 14 Feb 2007, Nick Schmansky wrote: > >> > >>> Anil, > >>> > >>> The image has almost no contrast. I've attached a TIFF of one slice. > >>> How was this acquired? Bruce, any idea why it would be so white? > >>> > >>> Nick > >>> > >>> > >>> On Wed, 2007-02-14 at 16:10 -0500, aroy85(a)gmail.com wrote: > >>>> The following files have been uploaded to the Martinos Center > FileDrop site > >>>> by Anil Roy for you to download: > >>>> > >>>> (1) orig.mgz > >>>> > >>>> > >>>> > >>>> These files will expire in 30 days. > >>>> > >>>> To view or download these files, go in your web browser to: > >>>> > >>>> > https://www.nmr.mgh.harvard.edu/facility/filedrop/showgroup/5010/426/7389dc… > >>>> > >>>> DO NOT SHARE this web address with anyone else. It is your personal > access key to the files. > >>>> > >>>> Overall Comment about files from Anil Roy: > >>>> > >>>> Hi, > >>>> > >>>> Attached is the orig.mgz file for the subject that quits at the > watershed step. > >>>> > >>>> Thanks, > >>>> > >>>> Anil. > >>>> > >>>> > >>> > >> > >> > > > > > > >

1 1

Jump to page:

2026

2025

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

2005

2004

Freesurfer